This is an automated message sent out weekly to report recent changes to Bioconductor packages. Please see the URL http://www.bioconductor.org/changelog.html for a complete history. ---------------------------------------------------------------------- - Feb 28, 2003: exprDB - dropped the exprs/se/calls database format to a vector of reals (i.e. a multichannel entry for each gene/array) with exprSets employing 2 channels. This should allow for better representation of affy and cDNA feature data, where the bigger memory problem lies. - BE Feb 28, 2003: affy - mas background now uses average of lowest 2% as background value rather than the 2% quantile - BMB Feb 27, 2003: added greenred.color as per user request Feb 26, 2003: tkWidgets - argsWidget allows the creation of a tk widgets for user to input arguments for a given R function. For example, argsWidget(formals("list.files")) creats a tk widget for inputing argements for function list.files. - JZ. Feb 26, 2003: Rgraphviz - Now allows for directed graphs Feb 24, 2003: graph/Rgraphviz - moved some of the plotting functionality back to Rgraphviz. JG

This is an automated message sent out weekly to report recent changes to Bioconductor packages. Please see the URL http://www.bioconductor.org/changelog.html for a complete history. ---------------------------------------------------------------------- - March 06, 2003: annotate - Added function 'pmAbst2html' which will take a list of pubMedAbst objects and create a simple web page. JG March 06, 2003: annotate - added some functions to annotate to make getting different identifiers more transparent. RG March 06, 2003: modified graph -- fixed some bugs and made boundary, subGraph and edges much faster. Added missing documentation. RG Mar 05, 2003: Biobase - Added a function createpackage() for the automatic creation of series of packages (e.g. cdf or ProbeTools packages for Affymetrix chips) from a set of template R, src, and man files. These may contain @PLACEHOLDERS@ to be filled in at the runtime of createpackage(). - WH Mar 05, 2003: tkWidgets/widgetTools - Put in a part in the first.lib which if the user is using Windows and can not load package 'tcltk', will point them to the R-Windows FAQ question 3.6 (on how to configure Tcl/Tk on their system), the most common cause of the problem. (devel & release1.1) - JG Mar 04, 2003: reposTools - Made the "versForce" option default to TRUE instead of FALSE. This gets rid of the effect where it would not install .zip based packages on Windows if they were built under a diff version of R. (devel & release1.1) - JG Mar 04, 2003: annotate - added a 'pmid' slot to the pubMedAbst class - JG Mar 04, 2003: Rgraphviz - added the 'neato' layout engine to the plots - JG Mar 03, 2003: exprDB - some fixes to improve compiling under older (gcc 2.96) compilers. Under RH7.1 this appears to require <float.h> -- BE Mar 01, 2003: affy - computeExprSet in Affybatch and expresso return an exprSet with an attribute 'pps.warnings'. method plot.ProbeSet. parameter 'scale' in barplot.ProbeSet... -- LG

This is an automated message sent out weekly to report recent changes to Bioconductor packages. Please see the URL http://www.bioconductor.org/changelog.html for a complete history. ---------------------------------------------------------------------- - March 13, 2003: annotate - locuslinkByID and locuslinkQuery now have a parameter "browse=TRUE". If TRUE (default), the behaviour is as it was before. If FALSE, the user's browser does not open up on the URL constructed, but rather will return the URL acquired. JG March 13, 2003: AnnBuilder - AnnBuilder has been modified to take advantage of the functions provided by pubRepo. A PostgreSQL database is no longer required. Examples of making annotation data packages are given in the vigenette. - JZ March 12, 2003: pubRepo - a new package for gettting/processing data from various public data libraries were added. Class pubRepo has functions to read data from a source url (using readLines), download data from a source url, and parse data from source url using a predefined parser and base file. Subclasses of pubRepo include LL(LocusLink), UG(UniGene), KEGG, GO(Gene Ontology), GEO(Gene Expression Omnibus), YG(Yease Genome), GP(GoldenPath) that may have methods for processing data for each repositoy. Documentation is not complete yet but will be ready soon. -JZ March 11, 2003: reposTools - winConvertSourceRepos now generates windows binary packages w/ the name structure of <pkg>.zip instead of <pkg>_<version>.zip. -JG

This is an automated message sent out weekly to report recent changes to Bioconductor packages. Please see the URL http://www.bioconductor.org/changelog.html for a complete history. ---------------------------------------------------------------------- -

This is an automated message sent out weekly to report recent changes to Bioconductor packages. Please see the URL http://www.bioconductor.org/changelog.html for a complete history. ---------------------------------------------------------------------- - March 28, 2003: Biobase - started removing and revising code to get ready for the next release March 28, 2003: getBioC - The parameter 'force', which was a version number force for binary packages has been moved to 'versForce', to more align with the reposTools parameters. Likewise, 'force' now corresponds to forcing a package to be installed even if all of its dependencies are not available. JG March 28, 2003: reposTools - An error in backpatching some changes caused a bug in the release branch which would throw an error when the R version did not match the R version the package was built under. (release1.1 only) JG March 27, 2003: annotate - Added a new function 'installDataPackage' which wraps the reposTools function install.packages2, to simply retrieve and install a requested Bioconductor data package. Also, the function pmAbst2html is now pmAbst2HTML. JG March 26, 2003: getBioC - added a 'method' parameter which works with the reposTools functions. JG March 25, 2003: reposTools - Added parameter 'method' to *.packages2 functions which is then passed on to the download.file calls used internally. This allows users to specify the 'wget' download method for files, useful if behind a proxy. (devel & release1.1) JG